Evaluating tools for transcription factor binding site prediction

Background: Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the mediation of transcriptional regulation. Information on experimentally validated functional TFBSs is limited and consequently there is a need for accurate prediction of TFBSs for gene annotation and in applications such as evaluating the effects of single nucleotide variations in causing disease. TFBSs are generally recognized by scanning a position weight matrix (PWM) against DNA using one of a number of available computer programs. Thus we set out to evaluate the best tools that can be used locally (and are therefore suitable for large-scale analyses) for creating PWMs from high-throughput ChIP-Seq data and for scanning them against DNA. Results: We evaluated a set of de novo motif discovery tools that could be downloaded and installed locally using ENCODE-ChIP-Seq data and showed that rGADEM was the best performing tool. TFBS prediction tools used to scan PWMs against DNA fall into two classes — those that predict individual TFBSs and those that identify clusters. Our evaluation showed that FIMO and MCAST performed best respectively. Conclusions: Selection of the best-performing tools for generating PWMs from ChIP-Seq data and for scanning PWMs against DNA has the potential to improve prediction of precise transcription factor binding sites within regions identified by ChIP-Seq experiments for gene finding, understanding regulation and in evaluating the effects of single nucleotide variations in causing disease

Интернационализация отечественного права в контексте правовых позиций Конституционного Суда Российской Федерации и Верховного Суда Российской Федерации

The article is aimed at identifying legal positions on the relationship between international and domestic Russian law in the decisions of Russian Constitutional Court and Russian Supreme Court.The purpose of the article is to confirm or disprove hypothesis that the practice of Russian Constitutional Court and Russian Supreme Court significantly changed the content of norm of Russian Constitution that recognizes generally recognized principles and norms of international law and international treaties as part of the Russian legal system.The methodological basis of the study was formed by both general scientific methods (dialectical, analysis and synthesis, induction and deduction) and special methods (synergistic, systemic-structural and formal-legal).The main results, scope of application. The main body of the article covers three interrelated issues. Firstly, the problems of interpretation of Pt. 4 of Art. 15 of the Russian Constitution. These problems are summarized to the ratio of the categories “generally recognized principles of international law” and “generally recognized norms of international law”, to possible contradictions between the current international treaty with the participation of Russia and the provisions of the Russian Constitution as well as to exceptions from the priority of international treaties over the domestic law of Russia. Five such exceptions are highlighted: the unconditional primacy of the Russian Constitution; domination of an international treaty only in the event of a conflict of its norms with the internal law of Russia; the presence in an international treaty of dispositive norms that are inferior to domestic law; taking into account the level of legal force when determining the correlation of an international treaty with the sources of national Russian law; implementation of an international treaty as self-executing or non-self-executing, when the priority of the latter directly depends on the adoption of an appropriate normative act of domestic law. Secondly, the system of legal positions of the Russian Constitutional Court on the relationship between international and domestic law and their target mission is considered. The legal positions on the issue under study are divided into two groups - on the interaction of international treaties with the domestic law of Russia and on the assessment of the prospects for the incorporation of the legal positions of the European Court of Human Rights into Russian legal system and the limits of its jurisdiction. The consolidating basis of all judicial legal positions is the unconditional priority of the Russian Constitution, the need to differentiate the normative content of an international treaty with the participation of the Russian Federation and acts of official interpretation by the authorized body of its norms, as well as the desire to preserve the constitutional identity of Russia. Thirdly, the subject of reflection was the limits of the internationalization of domestic law.Conclusions. There is an obstacle to the further internationalization of domestic law. It is the presence of spheres of public and state life that cannot and should not be included in the subject of international legal regulation and are subject exclusively to domestic legal impact. In addition, the framework of internationalization is due to the conflict with the state sovereignty of Russia and the desire to ensure the inviolability of the foundations of the constitutional order and national interests, and to ensure the country's constitutional identity.Посредством анализа законодательства, а также правовых позиций Конституционного Суда РФ и Верховного Суда РФ выявлены проблемы толкования ч. 4 ст. 15 Конституции РФ. Судебные правовые позиции по вопросам соотношения международного и отечественного права разделены на две группы: о взаимодействии международных договоров с внутренним правом России и об оценке инкорпорации правовых позиций Европейского Суда по правам человека в правовую систему России. Сделан вывод, что консолидирующими идеями всех судебных правовых позиций являются безусловный приоритет Конституции РФ, необходимость разграничения нормативного содержания международного договора с участием Российской Федерации и актов официального толкования уполномоченным органом его норм, а также стремление к сохранению конституционной самобытности России

Plasma Functionalization of Silica Bilayer Polymorphs

Ultrathin silica films are considered suitable two-dimensional model systems for the study of fundamental chemical and physical properties of all-silica zeolites and their derivatives, as well as novel supports for the stabilization of single atoms. In the present work, we report the creation of a new model catalytic support based on the surface functionalization of different silica bilayer (BL) polymorphs with well-defined atomic structures. The functionalization is carried out by means of in situ H-plasma treatments at room temperature. Low energy electron diffraction and microscopy data indicate that the atomic structure of the films remains unchanged upon treatment. Comparing the experimental results (photoemission and infrared absorption spectra) with density functional theory simulations shows that H2 is added via the heterolytic dissociation of an interlayer Si–O–Si siloxane bond and the subsequent formation of a hydroxyl and a hydride group in the top and bottom layers of the silica film, respectively. Functionalization of the silica films constitutes the first step into the development of a new type of model system of single-atom catalysts where metal atoms with different affinities for the functional groups can be anchored in the SiO2 matrix in well-established positions. In this way, synergistic and confinement effects between the active centers can be studied in a controlled manner

Growth and Atomic‐Scale Characterization of Ultrathin Silica and Germania Films: The Crucial Role of the Metal Support

The present review reports on the preparation and atomic‐scale characterization of the thinnest possible films of the glass‐forming materials silica and germania. To this end state‐of‐the‐art surface science techniques, in particular scanning probe microscopy, and density functional theory calculations have been employed. The investigated films range from monolayer to bilayer coverage where both, the crystalline and the amorphous films, contain characteristic XO4 (X=Si,Ge) building blocks. A side‐by‐side comparison of silica and germania monolayer, zigzag phase and bilayer films supported on Mo(112), Ru(0001), Pt(111), and Au(111) leads to a more general comprehension of the network structure of glass former materials. This allows us to understand the crucial role of the metal support for the pathway from crystalline to amorphous ultrathin film growth

Periodic ab initio estimates of the dispersive interaction between molecular nitrogen and a monolayer of hexagonal BN

The ab initio determination of the leading long-range term of pairwise additive dispersive interactions, based on the independent analysis of the response properties of the interacting objects, is here considered in the case where these are part of a periodic system. The interaction of a nitrogen molecule with a thin film of hexagonal BN has been chosen as a case study for identifying some of the problems involved, and for proposing techniques for their solution. In order to validate the results so obtained, the interaction energy between N2 and a BN monolayer at different distances has been estimated following a totally different approach, namely by performing post-Hartree–Fock (MP2) supercell calculations using the CRYSTAL+CRYSCOR suite of programs. The results obtained with the two approaches closely agree over a long range, while the limit of validity of the purely dispersive regime can be clearly assessed

Shared Metadata for Data-Centric Materials Science

The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps rather than hinders scientific work, the implementation of the FAIR-data principles (Findable, Accessible, Interoperable, and Reusable) must not be too narrow. Besides, the wider materials-science community ought to agree on the strategies to tackle the challenges that are specific to its data, both from computations and experiments. In this paper, we present the result of the discussions held at the workshop on "Shared Metadata and Data Formats for Big-Data Driven Materials Science". We start from an operative definition of metadata, and what features a FAIR-compliant metadata schema should have. We will mainly focus on computational materials-science data and propose a constructive approach for the FAIRification of the (meta)data related to ground-state and excited-states calculations, potential-energy sampling, and generalized workflows. Finally, challenges with the FAIRification of experimental (meta)data and materials-science ontologies are presented together with an outlook of how to meet them